I've found this with a bait I use from a very reputable and successful company - in fact I can't get a bite on anything else at the minute! Anyway there's been a couple of batches that have been slightly different in colour and scent and I asked the question, as you would. Apparently it is simply down to different fishmeals/krill and such that has fed differently prior to becoming an ingredient, thus making the flesh of the living creature develop differently. Makes logical sense to me and hasn't affected the bait I use.
Can't comment on the 3ft stuff, it seems to catch barbel but then again what doesn't??!